Bruce Adamson called on the Scottish and UK Governments to gather accurate data on the extent of the problem.
Ahead of a visit to a Dundee food bank on Tuesday, the commissioner praised schemes aimed helping children stay well fed in summer such as primary schools clubs across Glasgow and West Dunbartonshire and a summer holiday meals scheme in Dundee.
But he said holiday hunger should be eradicated.
Mr Adamson said: “While these schemes provide a vital safety net, we need to see holiday hunger within the broader context of poverty and food insecurity.
“The issue is not just about food. Holiday hunger and child poverty is a significant children’s rights issue in Scotland.
“A sustained, systematic and human rights-based approach at national and local level is needed to address and eradicate it. “
He added: “No child should be going hungry in the holidays. Children have a right to be free from hunger, food insecurity and malnutrition.
“Experiencing food insecurity as a child impacts negatively on physical health, mental health, and developmental outcomes and is a violation of their rights.
“It will shortly be the end of the school holidays and many children will have had a great summer break. Others will be less fortunate. For some children, school holidays can be a difficult time.
“Not only do they miss out on much of the play, culture, and informal education that the summer provides, many return to school in a worse state of health than at the start of the holidays which impacts on their ability to learn.
“It is not only having to pay for meals children usually get free at school, but there are additional costs for working parents.
“Then there are those hidden ‘holiday costs’ that many take for granted; days out and little treats.
“For many these are unaffordable luxuries as life simply becomes about surviving the holiday period, rather than enjoying it.
“Last year, the UN Committee on the Rights of the Child raised concerns that Scotland didn’t have accurate data on the scale of food insecurity.
“We are seeing the effects of this right now across Scotland - we know children are going hungry, yet we do not know the full extent of the problem.”